NM_000393.5(COL5A2):c.3690A>C (p.Thr1230=) AND not provided

Clinical significance:Benign (Last evaluated: Mar 17, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000393.5(COL5A2):c.3690A>C (p.Thr1230=)]

NM_000393.5(COL5A2):c.3690A>C (p.Thr1230=)

COL5A2:collagen type V alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000393.5(COL5A2):c.3690A>C (p.Thr1230=)
Other names:
  • NC_000002.12:g.189039507T>G
  • NG_011799.2:g.145373A>C
  • NG_011799.3:g.190795A>C
  • NM_000393.5:c.3690A>CMANE SELECT
  • NP_000384.2:p.Thr1230=
  • LRG_738t1:c.3690A>C
  • LRG_738:g.190795A>C
  • LRG_738p1:p.Thr1230=
  • NC_000002.11:g.189904233T>G
  • NM_000393.3:c.3690A>C
  • p.Thr1230Thr
dbSNP: rs10197596
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000393.5:c.3690A>C - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000696673Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
(Mar 17, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696673.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


Variant summary: The c.3690A>C (p.Thr1230=) in COL5A2 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant eliminates a cryptic acceptor cite, however no functional studies supporting these predictions were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.1081 (12897/119348 chrs tested), including numerous homozygous occurrences. This frequency exceeds the estimated maximum allele frequency for a pathogenic allele in this gene (0.0000063). The variant of interest hasbeen reported as Benign by multiple reputable databases/clinical laboratories. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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